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- PDB-6wag: Crystal Structure of SmcR S76A from Vibrio Vulnificus -

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Basic information

Entry
Database: PDB / ID: 6wag
TitleCrystal Structure of SmcR S76A from Vibrio Vulnificus
ComponentsLuxR family transcriptional regulator
KeywordsTRANSCRIPTION / quorum-sensing / transcription factor / DNA-binding protein
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.575 Å
AuthorsNewman, J.D. / Russell, M.M. / Gonzalez-Gutierrez, G. / van Kessel, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM124698 United States
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: The DNA binding domain of the Vibrio vulnificus SmcR transcription factor is flexible and binds diverse DNA sequences.
Authors: Newman, J.D. / Russell, M.M. / Fan, L. / Wang, Y.X. / Gonzalez-Gutierrez, G. / van Kessel, J.C.
History
DepositionMar 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LuxR family transcriptional regulator
B: LuxR family transcriptional regulator
C: LuxR family transcriptional regulator
D: LuxR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,8267
Polymers103,6054
Non-polymers2203
Water1,964109
1
A: LuxR family transcriptional regulator
B: LuxR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8653
Polymers51,8032
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-10 kcal/mol
Surface area19140 Å2
MethodPISA
2
C: LuxR family transcriptional regulator
D: LuxR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9614
Polymers51,8032
Non-polymers1582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-22 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.041, 99.039, 129.679
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
LuxR family transcriptional regulator / SmcR / SmcR-like protein / TetR/AcrR family transcriptional regulator / VvpR


Mass: 25901.363 Da / Num. of mol.: 4 / Mutation: S76A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria)
Gene: smcR, vvpR, CRN32_08135, CRN52_17705, D8T54_02235, D8T65_23975, JS86_16400
Production host: Escherichia coli (E. coli) / References: UniProt: Q9L8G8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M of Lithium Sulfate, 0.1 M Imidazole buffer pH 7.6-8 and 6-10% PEG3350
PH range: 7.6 - 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9763 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Aug 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.57→64.84 Å / Num. obs: 32493 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rpim(I) all: 0.067 / Rrim(I) all: 0.172 / Rsym value: 0.158 / Net I/σ(I): 10.2
Reflection shellResolution: 2.57→2.65 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1598 / CC1/2: 0.673 / Rpim(I) all: 0.672 / Rrim(I) all: 1.694 / Rsym value: 1.553 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.15_3459: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3kz9

3kz9


Resolution: 2.575→55.418 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 34.54
RfactorNum. reflection% reflection
Rfree0.2986 1674 5.19 %
Rwork0.2446 --
obs0.2474 32243 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.575→55.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6506 0 13 109 6628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046646
X-RAY DIFFRACTIONf_angle_d0.6339020
X-RAY DIFFRACTIONf_dihedral_angle_d1.743112
X-RAY DIFFRACTIONf_chiral_restr0.0421023
X-RAY DIFFRACTIONf_plane_restr0.0041173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5753-2.65110.39241400.33862490X-RAY DIFFRACTION99
2.6511-2.73670.35081390.31482512X-RAY DIFFRACTION99
2.7367-2.83450.35761470.29752507X-RAY DIFFRACTION100
2.8345-2.94790.33961440.28912518X-RAY DIFFRACTION100
2.9479-3.08210.36271350.28272551X-RAY DIFFRACTION100
3.0821-3.24460.31831200.26462543X-RAY DIFFRACTION100
3.2446-3.44780.32841320.25442542X-RAY DIFFRACTION100
3.4478-3.7140.36071570.28242434X-RAY DIFFRACTION95
3.714-4.08760.30021300.22592559X-RAY DIFFRACTION99
4.0876-4.67890.221440.18942568X-RAY DIFFRACTION100
4.6789-5.89380.23111420.22242621X-RAY DIFFRACTION100
5.8938-55.410.26531440.20742724X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.97154.76460.06715.6467-0.73493.19450.1046-0.49830.04570.0819-0.5581-0.4019-0.66740.67090.40520.5213-0.0692-0.0830.9833-0.04940.51134.136224.1218-1.3156
23.31970.2346-0.46152.4850.08583.4453-0.0514-0.00970.31180.14480.08840.1502-0.3059-0.38560.04860.25790.1192-0.0470.7498-0.07750.286117.12998.5933-13.0796
37.70632.98971.85582.51990.20743.3741-0.0284-0.6116-0.03390.092-0.1486-0.1549-0.03460.32160.1810.2837-0.02750.02840.8639-0.03930.394952.49112.027-19.3289
44.68370.2407-0.11321.777-1.18314.66110.08060.4057-0.074-0.1765-0.0875-0.00120.210.2770.01480.25090.05810.01740.6015-0.06910.224527.4642-1.8768-23.6444
55.83845.06012.54296.70993.2593.18340.3319-0.2129-0.17990.3472-0.1851-0.5781-0.13190.0978-0.11270.4105-0.0871-0.02240.6842-0.13210.378515.9204-26.86280.1389
63.6050.35630.43613.41490.04794.3745-0.1775-0.12380.11480.04860.0405-0.0307-0.29110.13380.13670.2395-0.04550.0110.5337-0.06160.17480.1572-41.6117-9.34
75.50221.07192.05763.71722.0552.4210.08880.68710.8052-0.1864-0.02680.5783-0.5215-0.7987-0.13410.31160.1645-0.00011.0101-0.02370.4271-5.4382-41.7492-22.6829
84.58940.49280.37344.11210.1033.4101-0.2824-1.6140.1261-0.07480.6213-0.51930.12420.4298-0.38740.4204-0.05370.03441.4728-0.18310.672838.0868-48.6614-16.0163
95.74850.2254-0.79751.3495-0.53933.3561-0.00550.1863-0.0436-0.19050.0141-0.14580.16620.7958-0.00230.29630.04370.01770.6176-0.07590.239411.4994-51.8614-23.6243
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 82 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 205 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 82 )
4X-RAY DIFFRACTION4chain 'B' and (resid 83 through 203 )
5X-RAY DIFFRACTION5chain 'C' and (resid 3 through 82 )
6X-RAY DIFFRACTION6chain 'C' and (resid 83 through 178 )
7X-RAY DIFFRACTION7chain 'C' and (resid 179 through 205 )
8X-RAY DIFFRACTION8chain 'D' and (resid 5 through 59 )
9X-RAY DIFFRACTION9chain 'D' and (resid 60 through 203 )

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